System analysis of Phycomyces light-growth response: madC, madG, and madH mutants.

The light-growth response of Phycomyces has been studied further with the sum-of-sinusoids method in the framework of the Wiener theory of nonlinear system identification. The response was treated as a black box with the logarithm of light intensity as the input and elongation rate as the output. The nonlinear input-output relation of the light-growth response can be represented mathematically by a set of weighting functions called kernels, which appear in the Wiener intergral series. The linear (first-order) kernels of wild type, and of single and double mutants affected in genes madA to madG were determined previously with Gaussian white noise test stimuli, and were used to investigate the interactions among the products of these genes (R.C. Poe, P. Pratap, and E.D. Lipson. 1986. Biol. Cybern. 55:105.). We have used the more precise sum-of-sinusoids method to extend the interaction studies, including both the first- and second-order kernels. Specifically, we have investigated interactions of the madH ("hypertropic") gene product with the madC ("night blind") and madG ("stiff") gene products. Experiments were performed on the Phycomyces tracking machine. The log-mean intensity of the stimulus was 6 x 10(-2) W m-2 and the wavelength was 477 nm. The first- and second-order kernels were analyzed in terms of nonlinear kinetic models.(ABSTRACT TRUNCATED AT 250 WORDS)     

Genetic analysis of hypertropic mutants of Phycomyces

A new class of Phycomyces behavioral mutants with enhanced tropic responses has been analyzed genetically to determine the number of genes involved and the nature of their expression. These hypertropic mutants carry pleiotropic nuclear mutations. Besides their effects on sensory behavior, they also affect morphology and meiotic processes. Behavioral analyses of heterokaryons containing hypertropic and wild-type nuclei in varying proportions show that the hypertropic mutations in strains L82, L84, L86, and L88 are strongly dominant. Conversely, the hypertropic mutations carried by the strains L83, L85, and L87 are strongly recessive. We performed recombination analyses between hypertropic mutants and mutants with diminished phototropism, affected in the seven genes madA to madG. We found no evidence of linkage between the hypertropic mutations and any of these mad mutations. From crosses, we isolated double mutants carrying hypertropic mutations together with madC (night blind) and madG (stiff) mutations. The behavioral phenotypes of the double mutants are intermediate between those of the parentals. Complementation analyses show that the three recessive hypertropic mutations affect the same gene, which we call madH. The expression of the recessive hypertropic allele becomes dominant in heterokaryons carrying madC and madH nuclei; the madC gene has been implicated separately with the photoreceptor at the input to the sensory pathway, while the madH gene is associated with the growth control output. This result suggests the physical interaction of both gene products, madH and madC, in a molecular complex for the photosensory transduction chain.     

Light and dark adaptation in Phycomyces phototropism

Light and dark adaptation of the phototropism of Phycomyces sporangiophores were analyzed in the intensity range of 10(-7)-6 W X m- 2. The experiments were designed to test the validity of the Delbruck- Reichardt model of adaptation (Delbruck, M., and W. Reichardt, 1956, Cellular Mechanisms in Differentiation and Growth, 3-44), and the kinetics were measured by the phototropic delay method. We found that their model describes adequately only changes of the adaptation level after small, relatively short intensity changes. For dark adaptation, we found a biphasic decay with two time constants of b1 = 1-2 min and b2 = 6.5-10 min. The model fails for light adaptation, in which the level of adaptation can overshoot the actual intensity level before it relaxes to the new intensity. The light adaptation kinetics depend critically on the height of the applied pulse as well as the intensity range. Both these features are incompatible with the Delbruck-Reichardt model and indicate that light and dark adaptation are regulated by different mechanisms. The comparison of the dark adaptation kinetics with the time course of the dark growth response shows that Phycomyces has two adaptation mechanisms: an input adaptation, which operates for the range adjustment, and an output adaptation, which directly modulates the growth response. The analysis of four different types of behavioral mutants permitted a partial genetic dissection of the adaptation mechanism. The hypertropic strain L82 and mutants with defects in the madA gene have qualitatively the same adaptation behavior as the wild type; however, the adaptation constants are altered in these strains. Mutation of the madB gene leads to loss of the fast component of the dark adaptation kinetics and to overshooting of the light adaptation under conditions where the wild type does not overshoot. Another mutant with a defect in the madC gene shows abnormal behavior after steps up in light intensity. Since the madB and madC mutants have been associated with the receptor pigment, we infer that at least part of the adaptation process is mediated by the receptor pigment.     

System analysis of Phycomyces light-growth response with sum-of-sinusoids test stimuli.

The light-growth response of Phycomyces has been studied with the sum-of-sinusoids method of nonlinear system identification (Victor, J.D., and R.M. Shapley, 1980, Biophys. J., 29:459). This transient response of the sporangiophore has been treated as a black-box system with one input (logarithm of the light intensity, I) and one output (elongation rate). The light intensity was modulated so that log I, as a function of time, was a sum of sinusoids. The log-mean intensity was 10(-4) W m-2 and the wavelength was 477 nm. The first- and second-order frequency kernels, which represent the linear and nonlinear behavior of the system, were obtained from the Fourier transform of the response at the appropriate component and combination frequencies. Although the first-order kernel accounts for most of the response, there remains a significant nonlinearity beyond the logarithmic transducer presumed to occur at the input of the sensory transduction chain. From the analysis of the frequency kernels, we have derived a dynamic nonlinear model of the light-growth response system. The model consists of a nonlinear subsystem followed by a linear subsystem. The model parameters were estimated from a combined nonlinear least-squares fit to the first- and second-order frequency kernels.     

White noise analysis of Phycomyces light growth response system. III. Photomutants.

Wiener kernels have been measured for the light growth response of a number of mutants of Phycomyces which show abnormal phototropism (mad mutants). Representative mutants were chosen from the six complementation groups (madA to madF) associated with the light response pathway. One group, madA, associated with the input part of the pathway, exhibits an essentially normal response provided it is tested above its moderate threshold. The groups madB and madC appear more defective, in that their kernel amplitudes are very small even above their thresholds. Their similarity to each other suggests a close functional connection between the respective genes. The remaining three groups (madD, madE, and madF) have all been associated with the output of the pathway. Tbe kernels for all three indicate a gain reduction, which depends gradually on intensity. These three groups appear to have the same absolute threshold as wild-type. None of the mutants studied shows special behavior at high intensity that could be evidence of alterations in the photoreceptor complex.     

System analysis of Phycomyces light-growth response: Single mutants

The white-noise method of system identification has been applied to the transient light-growth response of a set of seven mutants of Phycomyces with abnormal phototropism, affected in genes madA to madG. The Wiener kernels, which represent the input-output relation of the light-growth response, have been evaluated for each of these mutants and the wild-type strain at a log-mean blue-light intensity of 0.1 W m^-2. Additional experiments were done at 3x10^-4 and 10 W m^-2 on the madA strain C21 and wild-type. In the normal intensity range (0.1 W m^-2) the madA mutant behaves similarly to wild-type, but, at high intensity, the madA response is about twice as strong as that of wild-type. Except for C21 (madA), the first-order kernels of all mutants were smaller than the wild-type kernel. The first-order kernels for C111 (madB) and L15 (madC) show a prolonged time course, and C111 has a longer latency. The kernels for C110 (madE), C316 (madF), and C307 (madG) have a shallow and extended negative phase. For C68 (madD), the latency and time course are shorter than in the wild-type. These features are also reflected in the parameters estimated from fits of the anlytical model introduced in the previous paper to the experimental transfer functions (Fourier transforms of the kernels). The kernel for L15 (madC) is described better by a model that lacks one of the two second-order low-pass filters, because its response kinetics are dynamically of lower order.     

Threshold and adaptation in Phycomyces. Their interrelation and regulation by light

The absolute light sensitivity of Phycomyces sporangiophores was determined by analyzing the intensity dependence of the phototropic bending rate and of the light growth and dark growth responses to step changes of the intensity. We found that the different methods give approximately the same results for the wild-type strain, as well as for several behavioral mutants with defects in the genes madA, madB, and madC. A crucial factor in the determination of thresholds is the light intensity at which the strains grow during the 4 d after inoculation and prior to the experiment. When the wild-type strain grows in the dark, its threshold for the bending rate is 10(-9) W X m-2, compared with 2 X 10(-7) W X m-2 when it is grown under continuous illumination. Further, the maximal bending rate is twice as high in dark-grown strains. This phenomenon is further complicated by the fact that the diameter and growth rate of the sporangiophores also depend on the illumination conditions prior to the experiment: light-grown sporangiophores have an increased diameter and an increased growth rate compared with dark-grown ones. Some of the behavioral mutants, however, are indifferent to this form of light control. Another factor that is controlled by the growth conditions is adaptation: the kinetics of dark adaptation are slower in light-grown sporangiophores than in dark-grown ones. We found empirically a positive correlation between the slower dark adaptation constant and the threshold of the bending rate, which shows that the two underlying phenomena are functionally related.     

System analysis of Phycomyces light-growth response in single and double night-blind mutants

The sum-of-sinusoids method of nonlinear system identification has been applied to the light-growth response of the Phycomyces sporangiophore. Experiments were performed on the Phycomyces tracking machine with the wild-type strain with single and double mutants affected in genes madA, madB, and madC. The sum-of-sinusoids test stimuli were applied to the logarithm of the light intensity. The log-mean intensity level was 10^-1 Wm^-2 and the wavelength was 477 nm. The system identification results are in the form of first- and second-order frequency kernels, which are related to temporal kernels that appear in the Wiener functional series. The first-order kernels agree well with those obtained previously by the white noise method. In particular, the madA madB and madB madC double mutants show very weak responses. With the superior precision of the sum-of-sinusoids methods, we have achieved sufficient resolution to measure and analyze their second-order kernels. The first- and second-order frequency kernels were interpreted by system analysis methods involving a nonlinear parametric model. In addition a nonparametric hypothesis concerning interactions of gene products was tested. Results from the interaction tests confirm the earlier conclusion that the madB and madC gene products interact. In addition, with the enhanced precision and with the extension to nonlinear analysis, we have found evidence of interaction of the madA gene product with the madB and madC gene products. Thus all three genes appear to have mutual interactions, presumably because of their close physical association in a photoreceptor complex.     

Phycomyces: Phototropism and light-growth response to pulse stimuli

The relationship between phototropism and the light-growth response of Phycomyces blakesleeanus (Burgeff) sporangiophores was investigated. After dark adaptation, stage-IVb sporangiophores were exposed to short pulses of unilateral light at 450 nm wavelength. The sporangiophores show a complex reaction to pulses of 30 s duration: maximal positive bending at 3·10^-4 and 10^-1 J m^-2, but negative bending at 30 J m^-2. The fluence dependence for the light-growth response also is complex, but in a different way than for phototropism; the first maximal response occurs at 1.8·10^-3 J m^-2 with a lesser maximum at 30 J m^-2. A hypertropic mutant, L85 (madH), lacks the negative phototropism at 30 J m^-2 but gives results otherwise similar to the wild type. The reciprocity rule was tested for several combinations of fluence rates and pulse durations that ranged from 1 ms to 30 s. Near the threshold fluence (3·10^-5 J m^-2), both responses increase for pulse durations below 67 ms and both have an optimum at 2 ms. At a fluence of 2.4·10^-3 J m^-2, both responses decrease for pulse durations below 67 ms. The hypertropic mutant (madH), investigated for low fluence only, gave similar results. In both strains, the time courses for phototropism and light-growth response, after single short pulses of various durations, show no clear correlation. These results imply that phototropism cannot be caused by linear superposition of localized light-growth responses; rather, they point to redistribution of growth substances as the cause of phototropism.     

System analysis of Phycomyces light-growth response. Wavelength and temperature dependence.

The light-growth response of the Phycomyces sporangiophore was studied further with the sum-of-sinusoids method of nonlinear system identification. The first- and second-order frequency kernels, which represent the input-output relation of the system, were determined at 12 wavelengths (383-529 nm) and 4 temperatures (17 degrees, 20 degrees, 23 degrees, and 26 degrees C). The parametric model of the light-growth response system, introduced in the preceding paper, consists of nonlinear and linear dynamic subsystems in cascade. The model parameters were analyzed as functions of wavelength and temperature. At longer wavelengths, the system becomes more nonlinear. The latency and the bandwidth (cutoff frequency) of the system also vary significantly with wavelength. In addition, the latency decreases progressively with temperature (Q10 = 1.6). At low temperature (17 degrees C), the bandwidth is reduced. The results indicate that about half of the latency is due to physical processes such as diffusion, and the other half to enzymatic reactions. The dynamics of the nonlinear subsystem also vary with wavelength. The dependence of various model components on wavelength supports the hypothesis that the light-growth response, as well as phototropism, are mediated by multiple interacting photoreceptors.     

System analysis of Phycomyces light-growth response with gaussian white-noise test stimuli

The light-growth response of the Phycomyces sporangiophore is a transient change of elongation rate in response to changes in ambient blue-light intensity. The white-noise method of nonlinear system identification (Wiener-Lee-Schetzen theory) has been applied to this response, and the results have been interpreted by system analysis methods in the frequency domain. Experiments were performed on the Phycomyces tracking machine. Gaussian white-noise stimulus patterns were applied to the logarithm of the light intensity. The log-mean intensity of the broadband blue illumination was 0.1 W m^-2 and the standard deviation of the Gaussian white-noise was 0.58 decades. The results, in the form of temporal functions called Wiener kernels, represent the input-output relation of the light-growth response system. The transfer function, which was obtained as the Fourier transform of the first-order kernel, was analyzed in the frequency domain in terms of a dynamic model that consisted of a first-order high-pass filter, two secondorder low-pass filters, a delay element, and a gain factor. Parameters in the model (cutoff frequencies, damping coefficients, latency, and gain constant) were evaluated by nonlinear least-squares methods applied to the complex-valued transfer function. Analysis of the second-order kernel in the frequency domain suggests that the residual nonlinearity of the system lies close to the input.     

System analysis of Phycomyces light-growth response: Double mutants

The light-growth response of Phycomyces has been studied with Gaussian white-noise test stimuli for a set of 21 double mutants affected in all pairwise combinations of genes madA to madG; these genes are associated with phototropism, the light-growth response, and other behaviors. The input-output relations of the light-growth responses of these mutants are represented by Wiener kernels in the time domain and transfer functions in the frequency domain. The results have been analyzed comparatively with those in the preceding papers on wild-type and single mutant strains. Two of the double night-blind mutants (combinations AB and BC) have especially weak, but still detectable, responses. To evaluate possible dynamic interactions among the seven mad gene products, each double-mutant transfer function was analyzed jointly with those of the parental single mutants and wild-type. Specifically, a hypothesis of dynamic independence was rejected at the 5% significance level for the following combinations: AD, AE, AG, BC, BD, BE, BF, BG, CD, CE, CF, DE, DG, and EF. A formal pictorial scheme summarizes the dynamic interactions among the mad gene products, according to this test. The high degree of interactions between the input gene products (A, B, and C) and the output gene products (D, E, F, and G) suggest that most or all of the sensory transduction pathway for the light-growth response (and phototropism) is contained in a multimolecular complex.     

Blue light and phytochrome-mediated stomatal opening in the npq1 and phot1 phot2 mutants of Arabidopsis

Recent studies have shown that blue light-specific stomatal opening is reversed by green light and that far-red light can be used to probe phytochrome-dependent stomatal movements. Here, blue-green reversibility and far-red light were used to probe the stomatal responses of the npq1 mutant and the phot1 phot2 double mutant of Arabidopsis. In plants grown at 50 micromol m-2 s-1, red light (photosynthetic)-mediated opening in isolated stomata from wild type (WT) and both mutants saturated at 100 micromol m-2 s-1. Higher fluence rates caused stomatal closing, most likely due to photo-inhibition. Blue light-specific opening, probed by adding blue light (10 micromol m-2 s-1) to a 100 micromol m-2 s-1 red background, was found in WT, but not in npq1 or phot1 phot2 double mutant stomata. Under 50 micromol m-2 s-1 red light, 10 micromol m-2 s-1 blue light opened stomata in both WT and npq1 mutant stomata but not in the phot1 phot2 double mutant. In npq1, blue light-stimulated opening was reversed by far-red but not green light, indicating that npq1 has a phytochrome-mediated response and lacks a blue light-specific response. Stomata of the phot1 phot2 double mutant opened in response to 20 to 50 micromol m-2 s-1 blue light. This opening was green light reversible and far-red light insensitive, indicating that stomata of the phot1 phot2 double mutant have a detectable blue light-specific response.     

Chemotaxis mutants of Spirochaeta aurantia.

Five Spirochaeta aurantia chemotaxis mutants were isolated. One mutant (the che-101 mutant) never reversed, one (the che-200 mutant) flexed predominantly, two (the che-300 and che-400-1 mutants) exhibited elevated reversal frequencies, and one (the che-400 mutant) exhibited chemotactically unstimulated behavior similar to that of the wild-type strain. The che-101 and che-400 mutants were essentially nonchemotactic, whereas the che-200, che-300, and che-400-1 mutants showed impaired chemotactic responses. Protein methylation in response to attractant addition appeared normal in all of the mutants. Compared with the wild type, all of the mutants exhibited significantly altered membrane potential responses to the attractant xylose.     

Specific tropism caused by ultraviolet C radiation in Phycomyces

The giant sporangiophores of Phycomyces blakesleeanus turn towards blue and away from ultraviolet C sources (wavelength under 310 nm). We have isolated fifteen mutants with normal blue tropism but defective ultraviolet tropism. Wild-type sporangiophores described a double turn when exposed successively to blue and ultraviolet beams coming from the same side; under certain conditions, the mutants turned only to the blue. The new uvi mutations modified the behaviour in heterokaryosis and were lethal in homokaryosis, i.e., they affected essential cellular components. The responses of the wild type and one of the mutants were registered and evaluated with a computer-aided device. The mutant behaved normally under blue light, but took longer than the wild type to turn away from the ultraviolet source. With very weak ultraviolet stimuli (10(-8) and l0(-9) W m-2), the wild type turned towards the source, but the mutant did not respond. Calculations of absorbed-energy distributions in the sporangiophore showed that Phycomyces responds differently to similar spatial distributions of blue and ultraviolet radiations. Wild-type and mutant sporangiophores had the same high ultraviolet absorption due to gallic acid. We conclude that ultraviolet tropism is not just a modification of blue phototropism due to the high ultraviolet absorption of the sporangiophores. Phycomyces has a separate sensory system responsive to ultraviolet radiation, but not to blue light.     

White noise analysis of Phycomyces light growth response system. II. Extended intensity ranges.

By means of white gaussian noise stimulation, the Wiener kernels are derived for the Phycomyces light growth response for a variety of intensity conditions. In one experiment the intensity I, rather than log I, is used as the input variable. Under the very limited dynamic range of that experiment, the response is fairly linear. To examine the dependence of the kernels on dynamic range, a series of experiments were performed in which the range of log I was halved and doubled relative to normal. The amplitude of the kernels, but not the time course, is affected strongly by the choice of dynamic range, and the dependence reveals large-scale nonlinearities not evident in the kernels themselves. In addition kernels are evaluated for experiments at a number of absolute intensity levels ranging from 10(-12) to 10(-3) W/cm2. The kernel amplitudes are maximal at about 10(-6) W/cm2. At 10(-12) W/cm2, just above the absolute threshold, the respond is very small. The falloff at high intensity, attributable to inactivation of the photoreceptor, is analyzed in the framework of a first-order pigment kinetics model, yielding estimates for the partial extinction coefficient for inactivation epsilonI455 = (1.5 +/- 0.2) X 10(4) liter/mol-cm and a regeneration time constant of tau = (2.7 +/- 0.6) min. A model is introduced which associates the processes of adaptation and photoreceptor inactivation. The model predicts that the time constants for adaptation and pigment should be identical. This prediction is consistent with values in this and the preceding paper. The effects of pigment inactivation are simulated by a linear electronic analog circuit element, which may be cascaded with the linear simulator circuit in the preceding paper.     

Phototropism, Adaptation, and the Light-Growth Response of Phycomyces

Phototropic bending can be initiated without the transient changes in growth speed that characterize a light-growth response. The conditions required are a change from a symmetric to an asymmetric illumination pattern while the cell receives a constant radiant flux. Phototropism is thus basically a steady state process. It cannot be founded on differential light-growth responses as in Blaauw's theory. A possible model system for the unequal partition of growth during steady bending is discussed. The fact that light-growth responses show adaptation while phototropic bending does not follows from the different natures of the two responses.     

Multiple, independent components of ultraviolet radiation mutagenesis in Escherichia coli K-12 uvrB5.

Reversion systems involving the lacZ53(amber) and leuB19)missense) mutations were developed to study the mutant frequency response of Escherichia coli K-12 uvrB5 (SR250) to ultraviolet radiation (254 nm). A one-hit mutant frequency response was discernible at ultraviolet radiation fluences below approximately 0.5 J m-2. At higher fluences the overall mutant frequency response could be resolved into one-hit and two-hit components. A new interpretation of the published data on E. coli K-12 indicates that SR250 is not unique in this respect. In addition, the Lac reversion system showed enhanced mutagenesis after ultraviolet radiation fluences of approximately 1 to 3 J m-2, whereas the Leu reversion system did not. We conclude that the complex ultraviolet radiation mutant frequency response curves for E. coli K-12 uvrB5 were the result of three independent mutagenic processes for Lac reversion and two for Leu reversion.     

Growth rate fluctuations in phycomyces sporangiophores

The growth rate of the Phycomyces sporangiophore fluctuates under constant environmental conditions. These fluctuations underlie the well-characterized sensory responses to environmental changes. We compared growth fluctuations in sporangiophores of unstimulated wild type and behavioral mutants by use of maximum entropy spectral analysis, a mathematical technique that estimates the frequency and amplitude of oscillations in a time series. The mutants studied are believed to be altered near the input (“night-blind”) or output (“stiff” and “hypertropic”) of the photosensory transduction chain. The maximum entropy spectrum of wild type shows a sharp drop-off in spectral density above 0.3 millihertz, several minor peaks between 0.3 and 10 millihertz, and a broad maximum near 10 millihertz. Similar spectra were obtained for a night-blind mutant and a hypertropic mutant. In contrast, the spectra of three stiff mutants, defective in genes madD, madE, or madG, had distinctive peaks near 1.6 mHz and harmonics of this frequency. A madF stiff mutant, which is less stiff than madD, madE, and madG mutants, had a spectrum intermediate between wild type and the three other stiff mutants. Our results indicate that alterations in one or more steps associated with growth regulation output cause the Phycomyces sporangiophore to express a rhythmic growth rate.     

A cold-adapted protease engineered by experimental evolution system.

A new cold-adapted protease subtilisin BPN' mutant, termed m-51, was successfully isolated by use of an evolutionary program consisting of two-step in vitro random mutagenesis, which we developed for the screening of mutant subtilisins with increased activity at low temperature. The m-51 mutant showed 70% higher catalytic efficiency, expressed by the k(cat)/K(m) value, than the wild-type at 10 degrees C against N-succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide as a synthetic substrate. This cold-adaptation was achieved mainly by the increase in the k(cat) value in a temperature-dependent manner. Genetic analysis revealed that m-51 had three mutations, Ala-->Thr at position -31 (A-31T) in the prodomain, Ala-->Val at position 88 (A88V), and Ala-->Thr at position 98 (A98T). From kinetic parameters of the purified mutant enzymes, it was found that the A98T mutation led to 30% activity increase, which was enhanced up to 70% by the accompanying neutral mutation A88V. The A-31T mutation severely constrained the autoprocessing-mediated maturation of the pro-subtilisin in the Escherichia coli expression system, thus probably causing an activity-non-detectable mutation in the first step of mutagenesis. No distinct change was observed in the thermal stability of any mutant or in the substrate specificity for m-51. In the molecular models of the two single mutants (A88V and A98T), relatively large displacements of alpha carbon atoms were found around the mutation points. In the model of the double mutant (A88V/A98T), on the other hand, the structural changes around the mutation point counterbalanced each other, and thus no crucial displacements occurred. This mutual effect may be related to the enhanced activity of the double mutant.